CommonFunctions (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- stitching.CommonFunctions

public class CommonFunctions
extends Object

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`AVG`
`static String[]`	`colorList`
`static String[]`	`cpuMemSelect`
`static String[]`	`fusionMethodList`
`static String[]`	`fusionMethodListGrid`
`static String[]`	`fusionMethodListSimple`
`static int`	`LIN_BLEND`
`static int`	`MAX`
`static String[]`	`methodList`
`static String[]`	`methodListCollection`
`static int`	`MIN`
`static int`	`NONE`
`static int`	`RED_CYAN`
`static String[]`	`rgbTypes`
`static String[]`	`timeSelect`

Constructor Summary

Constructors
Constructor and Description

CommonFunctions()

Constructors
Constructor and Description
`CommonFunctions()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`addHyperLinkListener(MultiLineLabel text, String myURL)`
`static void`	`complexConjugate(float[] complex)`
`static FloatArray2D`	`computeFFT(FloatArray2D img)`
`static FloatArray3D`	`computeFFT(FloatArray3D img)`
`static float[]`	`computePhaseCorrelationMatrix(float[] fft1, float[] fft2, boolean inPlace)`
`static FloatArray2D`	`computePhaseCorrelationMatrix(FloatArray2D fft1, FloatArray2D fft2, int width)`
`static FloatArray3D`	`computePhaseCorrelationMatrix(FloatArray3D fft1, FloatArray3D fft2, int width)`
`static float`	`getPixelMin(int imageType, Object[] imageStack, int width, int height, int depth, int x, int y, int z, double min)`
`static int[]`	`getPixelMinRGB(Object[] imageStack, int width, int height, int depth, int x, int y, int z, double min)`
`static float`	`getPixelValueRGB(int rgb, int rgbType)`
`static double[]`	`getPlanePosition(IFormatReader r, MetadataRetrieve retrieve, int series, int t)`
`static double[]`	`getPlanePosition(IFormatReader r, MetadataRetrieve retrieve, int series, int t, boolean invertX, boolean invertY, boolean ignoreZStage)`
`static ij.ImagePlus`	`loadImage(String directory, String file, int seriesNumber)`
`static ij.ImagePlus`	`loadImage(String directory, String file, int seriesNumber, String rgb)`
`static float[]`	`multiply(float[] complexA, float[] complexB, boolean overwriteA)`
`static float`	`multiplyComplexImg(float a, float b, float c, float d)`
`static float`	`multiplyComplexReal(float a, float b, float c, float d)`
`static Thread[]`	`newThreads()`
`static Thread[]`	`newThreads(int numThreads)`
`static void`	`normalizeComplexVectorsToUnitVectors(float[] complex)`
`static ij.ImagePlus`	`openLOCIImagePlus(String path, String fileName, int seriesNumber)`
`static ij.ImagePlus`	`openLOCIImagePlus(String path, String fileName, int seriesNumber, String rgb)`
`static ij.ImagePlus`	`openLOCIImagePlus(String path, String fileName, int seriesNumber, String rgb, int from, int to)`
`static FloatArray2D`	`pffft2D(FloatArray2D values, boolean scale)`
`static FloatArray3D`	`pffft3DMT(FloatArray3D values, boolean scale)`
`static FloatArray2D`	`pffftInv2D(FloatArray2D values, int nfft)`
`static FloatArray3D`	`pffftInv3DMT(FloatArray3D values, int nfft)`
`static void`	`quicksort(Quicksortable[] data, int left, int right)`
`static void`	`startAndJoin(Thread[] threads)`
`static void`	`startTask(Runnable run, int numThreads)`
`static FloatArray2D`	`zeroPad(FloatArray2D ip, int width, int height)`
`static FloatArray3D`	`zeroPad(FloatArray3D ip, int width, int height, int depth)`
`static FloatArray2D[]`	`zeroPadImages(FloatArray2D img1, FloatArray2D img2)`
`static FloatArray3D[]`	`zeroPadImages(FloatArray3D img1, FloatArray3D img2)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

methodList
```
public static String[] methodList
```

AVG
```
public static final int AVG
```
See Also:

Constant Field Values

LIN_BLEND
```
public static final int LIN_BLEND
```
See Also:

Constant Field Values

MAX
```
public static final int MAX
```
See Also:

Constant Field Values

MIN
```
public static final int MIN
```
See Also:

Constant Field Values

RED_CYAN
```
public static final int RED_CYAN
```
See Also:

Constant Field Values

NONE
```
public static final int NONE
```
See Also:

Constant Field Values

methodListCollection

public static String[] methodListCollection

rgbTypes
```
public static String[] rgbTypes
```

colorList
```
public static String[] colorList
```

fusionMethodList

public static String[] fusionMethodList

fusionMethodListSimple

public static String[] fusionMethodListSimple

fusionMethodListGrid

public static String[] fusionMethodListGrid

timeSelect
```
public static String[] timeSelect
```

cpuMemSelect
```
public static String[] cpuMemSelect
```

Constructor Detail
- CommonFunctions
```
public CommonFunctions()
```

Method Detail

loadImage

public static ij.ImagePlus loadImage(String directory,
                                     String file,
                                     int seriesNumber)

loadImage

public static ij.ImagePlus loadImage(String directory,
                                     String file,
                                     int seriesNumber,
                                     String rgb)

addHyperLinkListener

public static final void addHyperLinkListener(MultiLineLabel text,
                                              String myURL)

openLOCIImagePlus

public static ij.ImagePlus openLOCIImagePlus(String path,
                                             String fileName,
                                             int seriesNumber,
                                             String rgb)

openLOCIImagePlus

public static ij.ImagePlus openLOCIImagePlus(String path,
                                             String fileName,
                                             int seriesNumber)

openLOCIImagePlus

public static ij.ImagePlus openLOCIImagePlus(String path,
                                             String fileName,
                                             int seriesNumber,
                                             String rgb,
                                             int from,
                                             int to)

getPixelValueRGB

public static float getPixelValueRGB(int rgb,
                                     int rgbType)

zeroPad

public static FloatArray3D zeroPad(FloatArray3D ip,
                                   int width,
                                   int height,
                                   int depth)

zeroPadImages

public static FloatArray3D[] zeroPadImages(FloatArray3D img1,
                                           FloatArray3D img2)

zeroPad

public static FloatArray2D zeroPad(FloatArray2D ip,
                                   int width,
                                   int height)

zeroPadImages

public static FloatArray2D[] zeroPadImages(FloatArray2D img1,
                                           FloatArray2D img2)

quicksort

public static void quicksort(Quicksortable[] data,
                             int left,
                             int right)

pffft2D

public static FloatArray2D pffft2D(FloatArray2D values,
                                   boolean scale)

pffftInv2D

public static FloatArray2D pffftInv2D(FloatArray2D values,
                                      int nfft)

pffft3DMT

public static FloatArray3D pffft3DMT(FloatArray3D values,
                                     boolean scale)

computePhaseCorrelationMatrix

public static FloatArray2D computePhaseCorrelationMatrix(FloatArray2D fft1,
                                                         FloatArray2D fft2,
                                                         int width)

computeFFT

public static FloatArray2D computeFFT(FloatArray2D img)

computePhaseCorrelationMatrix

public static FloatArray3D computePhaseCorrelationMatrix(FloatArray3D fft1,
                                                         FloatArray3D fft2,
                                                         int width)

computeFFT

public static FloatArray3D computeFFT(FloatArray3D img)

computePhaseCorrelationMatrix

public static float[] computePhaseCorrelationMatrix(float[] fft1,
                                                    float[] fft2,
                                                    boolean inPlace)

normalizeComplexVectorsToUnitVectors

public static void normalizeComplexVectorsToUnitVectors(float[] complex)

complexConjugate

public static void complexConjugate(float[] complex)

multiplyComplexReal

public static float multiplyComplexReal(float a,
                                        float b,
                                        float c,
                                        float d)

multiplyComplexImg

public static float multiplyComplexImg(float a,
                                       float b,
                                       float c,
                                       float d)

multiply

public static float[] multiply(float[] complexA,
                               float[] complexB,
                               boolean overwriteA)

pffftInv3DMT

public static FloatArray3D pffftInv3DMT(FloatArray3D values,
                                        int nfft)

startTask

public static void startTask(Runnable run,
                             int numThreads)

newThreads
```
public static Thread[] newThreads()
```

newThreads

public static Thread[] newThreads(int numThreads)

startAndJoin

public static void startAndJoin(Thread[] threads)

getPixelMinRGB

public static final int[] getPixelMinRGB(Object[] imageStack,
                                         int width,
                                         int height,
                                         int depth,
                                         int x,
                                         int y,
                                         int z,
                                         double min)

getPixelMin

public static final float getPixelMin(int imageType,
                                      Object[] imageStack,
                                      int width,
                                      int height,
                                      int depth,
                                      int x,
                                      int y,
                                      int z,
                                      double min)

getPlanePosition

public static final double[] getPlanePosition(IFormatReader r,
                                              MetadataRetrieve retrieve,
                                              int series,
                                              int t)

getPlanePosition

public static final double[] getPlanePosition(IFormatReader r,
                                              MetadataRetrieve retrieve,
                                              int series,
                                              int t,
                                              boolean invertX,
                                              boolean invertY,
                                              boolean ignoreZStage)

Class CommonFunctions

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

methodList

AVG

LIN_BLEND

MAX

MIN

RED_CYAN

NONE

methodListCollection

rgbTypes

colorList

fusionMethodList

fusionMethodListSimple

fusionMethodListGrid

timeSelect

cpuMemSelect

Constructor Detail

CommonFunctions

Method Detail

loadImage

loadImage

addHyperLinkListener

openLOCIImagePlus

openLOCIImagePlus

openLOCIImagePlus

getPixelValueRGB

zeroPad

zeroPadImages

zeroPad

zeroPadImages

quicksort

pffft2D

pffftInv2D

pffft3DMT

computePhaseCorrelationMatrix

computeFFT

computePhaseCorrelationMatrix

computeFFT

computePhaseCorrelationMatrix

normalizeComplexVectorsToUnitVectors

complexConjugate

multiplyComplexReal

multiplyComplexImg

multiply

pffftInv3DMT

startTask

newThreads

newThreads

startAndJoin

getPixelMinRGB

getPixelMin

getPlanePosition

getPlanePosition